diff --git a/modules/nf-core/pigz/compress/main.nf b/modules/nf-core/pigz/compress/main.nf
index 152e7006f46..7ccfa6e99a7 100644
--- a/modules/nf-core/pigz/compress/main.nf
+++ b/modules/nf-core/pigz/compress/main.nf
@@ -27,7 +27,7 @@ process PIGZ_COMPRESS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pigz:\$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
     END_VERSIONS
     """
 
@@ -39,7 +39,7 @@ process PIGZ_COMPRESS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pigz:\$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pigz/uncompress/main.nf b/modules/nf-core/pigz/uncompress/main.nf
index 11e43dff567..6e40e68b1c6 100644
--- a/modules/nf-core/pigz/uncompress/main.nf
+++ b/modules/nf-core/pigz/uncompress/main.nf
@@ -30,7 +30,7 @@ process PIGZ_UNCOMPRESS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
     END_VERSIONS
     """
 
@@ -38,11 +38,11 @@ process PIGZ_UNCOMPRESS {
     def args = task.ext.args ?: ''
     uncompressed_filename = zip.toString() - '.gz'
     """
-    touch ${zip.dropRight(3)}
+    touch $uncompressed_filename
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\w*//' ))
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pigz/uncompress/tests/main.nf.test b/modules/nf-core/pigz/uncompress/tests/main.nf.test
index 62ab27e2b64..9c3289bc0a2 100644
--- a/modules/nf-core/pigz/uncompress/tests/main.nf.test
+++ b/modules/nf-core/pigz/uncompress/tests/main.nf.test
@@ -29,5 +29,30 @@ nextflow_process {
         }
 
     }
+    
+    test("Should run without failures - stub") {
+        
+        options "-stub"
+        
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test'],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 
 }
\ No newline at end of file
diff --git a/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap b/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
index 126dd7d6a3c..bb4b5ee07cb 100644
--- a/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
+++ b/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
@@ -1,4 +1,37 @@
 {
+    "Should run without failures - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
+                ],
+                "file": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T14:42:44.906844906"
+    },
     "Should run without failures": {
         "content": [
             {
@@ -11,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,a2d5ce72baa8b303f25afb9cf094f683"
+                    "versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
                 ],
                 "file": [
                     [
@@ -22,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a2d5ce72baa8b303f25afb9cf094f683"
+                    "versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-15T16:43:21.55056643"
+        "timestamp": "2024-10-30T10:58:22.006893497"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/irmsd/meta.yml b/modules/nf-core/tcoffee/irmsd/meta.yml
index cf930ea038b..2cace48602b 100644
--- a/modules/nf-core/tcoffee/irmsd/meta.yml
+++ b/modules/nf-core/tcoffee/irmsd/meta.yml
@@ -26,11 +26,20 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', ... ]
+    - msa:
+        type: file
+        description: File containing the multiple sequence alignment
   - - meta2:
         type: map
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
+    - template:
+        type: file
+        description: File containing the template structure
+    - structures:
+        type: file
+        description: File containing the structures
 output:
   - irmsd:
       - meta: